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Series GSE193740 Query DataSets for GSE193740
Status Public on Feb 14, 2023
Title Gene silencing dynamics are modulated by transiently active regulatory elements [ChIP-seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Transcriptional enhancers have been extensively characterized, but cis-regulatory elements involved in acute gene repression have received less attention. Transcription factor GATA1 promotes erythroid differentiation by activating and repressing distinct gene sets. Here, we study the mechanism by which GATA1 silences the proliferative gene Kit during erythroid maturation, and define stages from initial loss of activation to heterochromatinization. We find that GATA1 inactivates a potent upstream enhancer but concomitantly creates a discrete intronic regulatory region marked by H3K27ac, short noncoding RNAs, and de-novo chromatin looping. This enhancer-like element forms transiently and serves to delay Kit silencing. The element is ultimately erased via engagement of the FOG1/NuRD deacetylase complex, as revealed by study of a disease-associated GATA1 variant. Hence, regulatory sites can be self-limiting by dynamic co-factor usage. Genome-wide analyses across cell types and species uncover transiently active elements at numerous genes during repression, suggesting that modulation of silencing kinetics is widespread.
 
Overall design Chromatin Immuno Precipitation (ChIP)-Sequencing at different time points of erythroid differentiation
 
Contributor(s) Vermunt MW
Citation(s) 36868189
Submission date Jan 14, 2022
Last update date May 16, 2023
Contact name Marit W. Vermunt
E-mail(s) vermuntmw@gmail.com
Organization name Children's Hospital of Phildelphia
Department Hematology
Lab Blobel
Street address 3615 Civic Center Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19146
Country USA
 
Platforms (2)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL30172 NextSeq 2000 (Mus musculus)
Samples (72)
GSM5819736 1991_G1E_H3K27ac_rep1
GSM5819737 2531_G1E_H3K27ac_rep2
GSM5819738 1992_G1E-ER4_-E2_H3K27ac_rep1
This SubSeries is part of SuperSeries:
GSE193825 Gene silencing dynamics are modulated by transiently active regulatory elements
Relations
BioProject PRJNA797444

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Supplementary file Size Download File type/resource
GSE193740_RAW.tar 8.5 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
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